The fact they made her a bit tough at the beggining (which instantly makes. people forget about the kitty cupcakes, i mean there KITTY cupcakes.) just drives people to believe shes the "Rude" one, since some could consider Sayori the "Cute".

But you could also blame Dan Salvato for the lack of pure story she gets, sure we hear that her father abuses her, but at least add a bit that proves that (Even the wiki says "It hints at" Natsuki's father abusing her). Just that would flesh the game out and make it a slightly better experience for most people.